Chlamydia trachomatis is the leading cause of preventable blindness in developing countries and the most commonly reported sexually transmitted infection worldwide. Chlamydia pneumoniae is the cause of approximately 10% of community-acquired respiratory infections worldwide. C. trachomatis and C. pneumoniae have been implicated in more serious disease sequelae that have been proposed to arise due to chronic inflammatory conditions associated with persistent infections. The cytokine IFN-? plays a central role in controlling chlamydial infections and has been shown to induce a persistent growth state in cell culture models. Persistent growth in the presence of IFN-? has been shown to block the normal developmental cycle of the organisms and prevent the differentiation of the organism to the infectious form. We plan to study the role of a family of non-coding RNAs in the developmental cycle and the changes associated with IFN- ?- induced persistent growth. The hypothesis to be tested is that ncRNAs play an important role in the developmental cycle and are centrally involved in the changes associated with persistent growth in the presence of IFN-?. Non-coding RNAs will be identified using intergenic and genome-wide tiling microarrays and will be confirmed by Northern analysis and transcript mapping procedures. The mechanism of action of the confirmed non-coding RNAs will be studied using co-expression studies in Escherichia coli. Finally, the regulatory roles of non-coding RNAs will be tested during normal and IFN-?-induced persistent growth of C. trachomatis and C. pneumoniae using microarray analysis, quantitative gene expression analysis and combined gene expression and protein expression studies. The proposed work will result in a more complete understanding of the developmental cycle of C. trachomatis and C. pneumoniae and will lead to a mechanistic understanding of the chlamydial response to the human innate immune-response. Regulatory RNAs represent a new class of targets for non-traditional antibacterials in a rapidly developing field of study. Narrative: The pathogenic chlamydiae are responsible for respiratory disease, sexually transmitted disease, blinding trachoma and associated chronic diseases. This project uses genome level analyses to determine the role of a new class of RNA regulators in normal growth and the response of the bacteria to the host's immune system. These regulators control important aspects of the bacteria's response to its environment and their role in normal and chronic forms of infection will be studied.